It's pretty easy to tell human DNA from bacterial DNA. For one thing bacteria have small circular genomes versus huge linear chromosomes. More importantly individual sequencing for humans is heavily assisted by aligning reads to a known genome so any sequences which don't resemble known human DNA will probably be discarded.
I cant speak to whether they are actually sequencing samples, but it'd be a pretty blatant lie if they're not.
You basically take all the dna in the sample and chop it all into small pieces and all of these small pieces are read into computer memory, and then an algorithm goes through them all and merges the pieces that fit together back together into the original long form of the dna. Only pieces that have overlaps with each other will merge together, and there are many redundancies, so if any pieces accidentally fit together that aren't actually supposed to, then they are discarded, because this won't happen nearly as often as the real merge.
So maybe a bunch of human dna gets mixed up with bacterial dna - I dunno really - but it really doesn't matter because of the way they put back together.
The two basic ways to deal with bacterial contamination in NGS sequencing is to minimize it during extraction (e.g. extracting DNA from isolated nuclei, which bacteria do not have) and to clean up the raw reads by comparing them to known microbial sequences (e.g. with http://deconseq.sourceforge.net/ )
Considering they offer the raw data on a 500GB hard drive in a FASTAQ format (https://us.dantelabs.com/pages/faq), I doubt it's just SNPs.
"Blood samples had 5-6% unmapped reads compared to 7-18% in saliva. Evaluation of source of unmapped reads found that 0.54% mapped to viral species in both sample types. In contrast, 10.3% of unmapped reads from saliva samples mapped to bacterial species, compared with only 1% of unmapped reads from blood samples as expected1. This analysis represents, to our knowledge, the first comprehensive examination of WGS and WES data generated from blood compared to saliva. Our analysis shows a high level of concordance between the two sample sources, and as expected few somatic variants. This indicates that high quality sequencing data can be derived from saliva samples for germline genetic analyses." [1]
and
"SNP genotyping results for saliva derived DNA (n = 39) illustrated a 98.7% concordance when compared with blood DNA. In conclusion, when compared with blood DNA and tested on the DMET array, saliva-derived DNA provided adequate genotyping quality with a significant lower number of SNP calls. Saliva-derived DNA does perform very well if it contains greater than 31.3% human amplifiable DNA." [2]
Frankly I don't think they bother. It's not a huge issue.
Sequencing will run to a certain coverage (or depth), aligning multiple fragments so that each nucleotide is sampled e.g. 30 times, which would weed out contaminants. Saliva is generally considered 'good enough' (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497576/)
They might just use an anti-microbial agent in their collection kit to prevent growth of bacteria until it reaches their lab (plus you don't want bacterial nucleases to fragment your DNA).
